A global proteome study of Mycobacterium gilvum PYR-GCK grown on pyrene and glucose reveals the activation of glyoxylate, shikimate and gluconeogenetic pathways through the central carbon metabolism highway

The Combination of Buchloe dactyloides Engelm and Biochar Promotes the Remediation of Soil Contaminated with Polycyclic Aromatic Hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) cause serious stress to biological health and the soil environment as persistent pollutants. Despite the wide use of biochar in promoting soil improvement, the mechanism of biochar removing soil PAHs through rhizosphere effect in the process of phytoremediation remain uncertain. In this study, the regulation of soil niche and microbial degradation strategies under plants and biochar were explored by analyzing the effects of plants and biochar on microbial community composition, soil metabolism and enzyme activity in the process of PAH degradation. The combination of plants and biochar significantly increased the removal of phenanthrene (6.10%), pyrene (11.50%), benzo[a]pyrene (106.02%) and PAHs (27.10%) when compared with natural attenuation, and significantly increased the removal of benzo[a]pyrene (34.51%) and PAHs (5.96%) when compared with phytoremediation. Compared with phytoremediation, the combination of plants and biochar significantly increased soil nutrient availability, enhanced soil enzyme activity (urease and catalase), improved soil microbial carbon metabolism and amino acid metabolism, thereby benefiting microbial resistance to PAH stress. In addition, the activity of soil enzymes (dehydrogenase, polyphenol oxidase and laccase) and the expression of genes involved in the degradation and microorganisms (streptomyces, curvularia, mortierella and acremonium) were up-regulated through the combined action of plants and biochar. In view of the aforementioned results, the combined application of plants and biochar can enhance the degradation of PAHs and alleviate the stress of PAH on soil microorganisms.

Biosurfactants-based mixed polycyclic aromatic hydrocarbon degradation: From microbial community structure toward non-targeted metabolomic profile determination

Biosurfactants-based bioremediation is considered an efficient technology to eliminate environmental pollutants including polycyclic aromatic hydrocarbons (PAHs). However, the precise role of rhamnolipids or lipopeptide-biosurfactants in mixed PAH dissipation, shaping microbial community structure, and influencing metabolomic profile remained unclear. In this study, results showed that the maximum PAH degradation was achieved in lipopeptide-assisted treatment (SPS), where the pyrene and phenanthrene were substantially degraded up to 74.28 % and 63.05 % respectively, as compared to rhamnolipids (SPR) and un-aided biosurfactants (SP). Furthermore, the high throughput sequencing analysis revealed a significant change in the PAH-degrading microbial community, with Proteobacteria being the predominant phylum (>98 %) followed by Bacteroidota and Firmicutes in all the treatments. Moreover, Pseudomonas and Pannonibacter were found as highly potent bacterial genera for mixed PAH degradation in SPR, SPS, and SP treatments, nevertheless, the abundance of the genus Pseudomonas was significantly enhanced (>97 %) in SPR treatment groups. On the other hand, the non-targeted metabolomic profile through UHPLC-MS/MS exhibited a remarkable change in the metabolites of amino acids, carbohydrates, and lipid metabolisms by the input of rhamnolipids or lipopeptide-biosurfactants whereas, the maximum intensities of metabolites (more than two-fold) were observed in SPR treatment. The findings of this study suggested that the aforementioned biosurfactants can play an indispensable role in mixed PAH degradation as well as seek to offer new insights into shifts in PAH-degrading microbial communities and their metabolic function, which can guide the development of more efficient and targeted strategies for complete removal of organic pollutants such as PAH from the contaminated environment.

Metagenomics reveals mechanism of pyrene degradation by an enriched bacterial consortium from a coking site contaminated with PAHs

A bacterial consortium, termed WPB, was obtained from polycyclic aromatic hydrocarbons (PAHs) contaminated soil from a coking site. The consortium effectively degraded 100 mg L-1 pyrene by 94.8 % within 12 days. WPB was also able to degrade phenanthrene (98.3 %) and benzo[a]pyrene (24.6 %) in 12 days, while the individual isolates showed no PAHs degrading ability. Paracoccus sp. dominated the bacterial consortium (65.0-86.2 %) throughout the degradation process. Metagenomic sequencing reveals the proportion of sequences with xenobiotics biodegradation and metabolism increased throughout the degradation process indicating the great potential of WPB to degrade pollutants. The annotation of genes by metagenomic analysis help reconstruct the degradation pathways ("phthalate pathway" and "naphthalene degradation") and reveal how different bacteria contribute to the degradation process. Mycobacterium gilvum was found to carry nidAB genes that catalyze the first step of high-molecular-weight (HMW) PAHs in the degradation process despite Mycobacterium gilvum accounting for only 0.005-0.06 %. In addition, genomes of Paracoccus denitrificans and some other genera affiliated with Devosia, Pusillimonas caeni and Eoetvoesia caeni were successfully recovered and were found to carry genes responsible for the degradation of the intermediates of pyrene. These results enable further understanding of the metabolic patterns of pyrene-degrading consortia and provide direction for further cultivation and discovery of key players in complex microbial consortia.

Multi-Approach Characterization of Novel Pyrene-Degrading Mycolicibacterium austroafricanum Isolates Lacking nid Genes

Polycyclic aromatic hydrocarbons (PAHs) are chemical compounds that are widespread in the environment, arising from the incomplete combustion of organic material, as well as from human activities involving petrol exploitation, petrochemical industrial waste, gas stations, and environmental disasters. PAHs of high molecular weight, such as pyrene, have carcinogenic and mutagenic effects and are considered pollutants. The microbial degradation of PAHs occurs through the action of multiple dioxygenase genes (nid), which are localized in genomic island denominate region A, and cytochrome P450 monooxygenases genes (cyp) dispersed in the bacterial genome. This study evaluated pyrene degradation by five isolates of Mycolicibacterium austroafricanum using 2,6-dichlorophenol indophenol (DCPIP assay), gas chromatography/mass spectrometry (CG/MS), and genomic analyses. Two isolates (MYC038 and MYC040) exhibited pyrene degradation indexes of 96% and 88%, respectively, over a seven-day incubation period. Interestingly, the genomic analyses showed that the isolates do not have nid genes, which are involved in PAH biodegradation, despite their ability to degrade pyrene, suggesting that degradation may occur due to the presence of cyp150 genes, or even genes that have not yet been described. To the best of our knowledge, this is the first report of isolates without nid genes demonstrating the ability to degrade pyrene.

Genome sequence of Stenotrophomonas indicatrix CPHE1, a powerful phenanthrene-degrading bacterium

Environmental pollution caused by polycyclic aromatic hydrocarbons (PAHs) involves a high-risk and have received considerable attention due to their carcinogenic, teratogenic, and mutagenic properties. Phenanthrene (PHE) is a low molecular weight PAH, which has three benzene rings. It is one of the most common PAH found in contaminated environments mainly due to its low volatilization ability and hydrophobic character. A PHE degrading bacterium was isolated from an industrial contaminated soil using enrichment culture techniques. Based on macroscopic, microscopic examination and phylogenetic analysis, this bacterium was classified as Stenotrophomonas indicatrix and named strain CPHE1. Several authors have reported about bacteria stains, which can degrade PHE, but this is the first time where the ability of S. indicatrix to biodegrade and mineralize PHE has been demonstrated.

Metagenomic Analysis of Microbial Alliances for Efficient Degradation of PHE: Microbial Community Structure and Reconstruction of Metabolic Network

Polycyclic aromatic hydrocarbons are a widespread organic pollutant worldwide. In this study, a highly efficient phenanthrene (PHE)-degrading microbial community was enriched from oil extraction soil, which could degrade 500 mg/L PHE within 4 days. Using 16S rRNA sequencing, the dominant bacteria in this community at the phylum level were found to be Proteobacteria, Actinobacteria, and Firmicutes. Metagenomic annotation of genes revealed the metabolic pathways and the contribution of different bacteria to the degradation process. Pseudomonadaceae contributed multiple functional genes in the degradation process. This study revealed the functional genes, metabolic pathways, and microbial interactions of the microbial community, which are expected to provide guidance for practical management.

Soil bacterial diversity and functionality are driven by plant species for enhancing polycyclic aromatic hydrocarbons dissipation in soils

Plant-microorganisms symbiosis has been widely used in developing strategies for the rhizoremediation of polycyclic aromatic hydrocarbon (PAHs) contaminated agricultural soils. However, understanding the potential mechanisms for using complex plant-microbe interactions to enhance rhizoremediation in contaminated soils is still limited. In this study, rhizosphere microbiomes were established by cultivating four types of cover crops for 15 months in a PAHs-contaminated field. The results showed that the PAHs removal rates were significantly higher in rhizosphere soils (55.2-82.3%) than the bare soils (20.5%). Of the four cover crops, the rhizosphere soils associated with the alfalfa and clover had higher removal rates for high molecular weight (HMW) PAHs (78.5-87.1%) than the grasses (39.0-46.2%). High-throughput sequencing analysis showed that bacterial community structure between the planted and bare soils, and among four cover crops rhizosphere soils were significantly different. The rhizosphere soils associated with the alfalfa and clover had more abundant degradation-related taxa. Correlation network analysis showed that bacterial communities with high removal rates have stronger interactions. Metagenome analysis indicated that the relative abundance of the key functional genes involved in PAHs degradation and nutrient metabolisms were significantly higher in rhizosphere soils, especially for alfalfa and clover. Overall, this study provides new insights for us to understand the mechanisms by different plants enhancing PAHs dissipation from the viewpoint of microbiology.

Bioaugmentation strategy to enhance polycyclic aromatic hydrocarbons anaerobic biodegradation in contaminated soils

This paper proposes an innovative bioaugmentation approach for the remediation of polycyclic aromatic hydrocarbon (PAH) contaminated soils, based on a novel habitat-based strategy. This approach was tested using two inocula (i-24 and i-96) previously enriched through an anaerobic digestion process on wheat straw. It relies on the application of allochthonous microorganisms characterized by specific functional roles obtained by mimicking a natural hydrolytic environment such as the rumen. The inocula efficiency was tested in presence of naphthalene alone, benzo[a]pyrene alone, and a mix of both of them. In single-contamination tests, i-24 inoculum showed the highest biodegradation rates (84.7% for naphthalene and 51.7% for benzo[a]pyrene). These values were almost 1.2 times higher than those obtained for both contaminants with i-96 inoculum and in the control test in presence of naphthalene alone, while they were 3 times higher compared to the control test in presence of benzo[a]pyrene alone. In mixed-contamination tests, i-96 inoculum showed final biodegradation efficiencies for naphthalene and benzo[a]pyrene between 1.1 and 1.5 higher than i-24 inoculum or autochthonous biomass. Total microbial abundances increased in the bioaugmented tests in line with the PAH degradation. The microbial community structure showed the highest diversity at the end of the experiment in almost all cases. Values of the Firmicutes active fraction up to 7 times lower were observed in the i-24 bioaugmented tests compared to i-96 and control tests. This study highlights a successful bioaugmentation strategy with biological components that can be reused in multiple processes supporting an integrated and environmentally sustainable bioremediation system.

Insights into the mechanisms underlying efficient Rhizodegradation of PAHs in biochar-amended soil: From microbial communities to soil metabolomics

The combined effects of biochar amendment and the rhizosphere on the soil metabolic microbiome during the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil remain unknown. In this study, we attempted to characterize a PAH degradation network by coupling the direct PAH degradation with soil carbon cycling. From microbial community structure and functions to metabolic pathways, we revealed the modulation strategies by which biochar and the rhizosphere benefited PAH degradation in soil. Firstly, some PAH degraders were enriched by biochar and the rhizosphere, and their combination promoted the cooperation among these PAH degraders. Simultaneously, under the combined effects of biochar and the rhizosphere, the functional genes participating in upstream PAH degradation were greatly upregulated. Secondly, there were strong co-occurrences between soil microbial community members and metabolites, in particular, some PAH degraders and the metabolites, such as PAH degradation products or common carbon resources, were highlighted in the networks. It shows that the overall downstream carbon metabolism of PAH degradation was also greatly upregulated by the combined effects of biochar and plant roots, showing good survival of the soil microbiome and contributing to PAH biodegradation. Taken together, both soil carbon metabolism and direct contaminant biodegradation are likely to be modulated by the combined effects of biochar and plant roots, jointly benefitting to PAH degradation by soil microbiome. Our study is the first to link PAH degradation with native carbon metabolism by coupling sequencing and soil metabolomics technology, providing new insights into a systematic understanding of PAH degradation by indigenous soil microbiome and their networks.

A comprehensive study of conditions of the biodegradation of a plastic additive 2,6-di-tert-butylphenol and proteomic changes in the degrader Pseudomonas aeruginosa san ai

The Pseudomonas aeruginosa san ai strain was investigated for its capability to degrade the 2,6-di-tert-butylphenol (2,6-DTBP) plastic additive, a hazardous and toxic substance for aquatic life. This investigation was performed under different parameter values: 2,6-DTBP concentration, inoculum size, pH, and temperature. The GC-MS study showed that P. aeruginosa efficiently degraded 2,6-DTBP in the pH range of 5-8 at higher temperatures. Under exposure to 2,6-DTBP concentrations of 2, 10, and 100 mg L-1, the strain degraded by 100, 100, and 85%, respectively, for 7 days. Crude enzyme preparation from the biomass of P. aeruginosa san ai showed higher efficiency in 2,6-DTBP removal than that shown by whole microbial cells. Gene encoding for the enzymes involved in the degradation of aromatic compounds in P. aeruginosa san ai was identified. To complement the genomic data, a comparative proteomic study of P. aeruginosa san ai grown on 2,6-DTBP or sunflower oil was conducted by means of nanoLC-MS/MS. The presence of aromatic substances resulted in the upregulation of aromatic ring cleavage enzymes, whose activity was confirmed by enzymatic tests; therefore, it could be concluded that 2,6-DTBP might be degraded by ortho-ring cleavage. A comparative proteomics study of P. aeruginosa san ai indicated that the core molecular responses to aromatic substances can be summarized as the upregulation of proteins responsible for amino acid metabolism with emphasized glutamate metabolism and energy production with upregulated enzymes of glyoxylate bypass. P. aeruginosa san ai has a high capacity to efficiently degrade aromatic compounds, and therefore its whole cells or enzymes could be used in the treatment of contaminated areas.

Metabolomics of colistin methanesulfonate treated Mycobacterium tuberculosis

Over the past 5 years, there has been a renewed interest in finding new compounds with anti-TB action. Colistin methanesulfonate or polymyxin E, is a possible anti-TB drug candidate, which may in future be used either alone or in combination to the current 6 month "directly observed treatment short-course" (DOTS) regimen. However its mechanism of action has to date not yet been fully explored, and only described from a histological and genomics perspective. Considering this, we used a GCxGC-TOFMS metabolomics approach and identified those metabolite markers characterising Mycobacterium tuberculosis (Mtb) cultured in the presence of colistin methanesulfonate, in order to better understand or confirm its mechanism of action. The metabolite markers identified indicated a flux in the metabolism of the colistin methanesulfonate treated Mtb towards fatty acid synthesis and cell wall repair, confirming previous reports that colistin acts by disrupting the cell wall of mycobacteria. Accompanying this, is a subsequently elevated glucose uptake, since the latter now serves as the primary energy substrate for the upregulated glyoxylate cycle, and additionally as a precursor for further fatty acid synthesis via the glycerolipid metabolic pathway. Furthermore, the elevated concentrations of those metabolites associated with pentose phosphate, valine, threonine, and pentanediol metabolism, also confirms a shift towards glucose utilization for energy production, in the colistin methanesulfonate treated Mtb.

Elucidating the antimicrobial mechanisms of colistin sulfate on Mycobacterium tuberculosis using metabolomics

Considering the disadvantageous of first line anti-tuberculosis (TB) drugs, including poor patient adherence, drug side effects, the long treatment duration and rapidly increasing microbe resistance, alternative treatment strategies are needed. Colistin sulfate (CS), a polymyxin antibiotic considered a last-resort antibiotics for treating multidrug-resistant Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter, has antimicrobial activity towards mycobacteria, and could serve as a possible anti-TB drug. Using GCxGC-TOFMS metabolomics, we compared the metabolic profiles of Mycobacterium tuberculosis (Mtb) cultured in the presence and absence of CS, to elucidate the mechanisms by which this drug may exert its antimicrobial effects. The principal component analysis of the metabolite data indicated significant variation in the underlying metabolite profiles of the groups. Those metabolites best explaining this differentiation, were acetic acid, and cell wall associated methylated and unmethylated fatty acids, and their alcohol and alkane derivatives. The elevated glucose levels, and various glyoxylate and glycerolipid metabolic intermediates, indicates an elevated flux in these metabolic pathways. Since all the metabolites identified in the colistin treated Mtb indicates an increase in fatty acid synthesis and cell wall repair, it can be concluded that CS acts by disrupting the cell wall in Mtb, confirming a similar drug action to other organisms.

Comparative functional pan-genome analyses to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon metabolism in the genus Mycobacterium

Background

The bacterial genus Mycobacterium is of great interest in the medical and biotechnological fields. Despite a flood of genome sequencing and functional genomics data, significant gaps in knowledge between genome and phenome seriously hinder efforts toward the treatment of mycobacterial diseases and practical biotechnological applications. In this study, we propose the use of systematic, comparative functional pan-genomic analysis to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon (PAH) metabolism in the genus Mycobacterium.

Results

Phylogenetic, phenotypic, and genomic information for 27 completely genome-sequenced mycobacteria was systematically integrated to reconstruct a mycobacterial phenotype network (MPN) with a pan-genomic concept at a network level. In the MPN, mycobacterial phenotypes show typical scale-free relationships. PAH degradation is an isolated phenotype with the lowest connection degree, consistent with phylogenetic and environmental isolation of PAH degraders. A series of functional pan-genomic analyses provide conserved and unique types of genomic evidence for strong epistatic and pleiotropic impacts on evolutionary trajectories of the PAH-degrading phenotype. Under strong natural selection, the detailed gene gain/loss patterns from horizontal gene transfer (HGT)/deletion events hypothesize a plausible evolutionary path, an epistasis-based birth and pleiotropy-dependent death, for PAH metabolism in the genus Mycobacterium. This study generated a practical mycobacterial compendium of phenotypic and genomic changes, focusing on the PAH-degrading phenotype, with a pan-genomic perspective of the evolutionary events and the environmental challenges.

Conclusions

Our findings suggest that when selection acts on PAH metabolism, only a small fraction of possible trajectories is likely to be observed, owing mainly to a combination of the ambiguous phenotypic effects of PAHs and the corresponding pleiotropy- and epistasis-dependent evolutionary adaptation. Evolutionary constraints on the selection of trajectories, like those seen in PAH-degrading phenotypes, are likely to apply to the evolution of other phenotypes in the genus Mycobacterium.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0302-8) contains supplementary material, which is available to authorized users.

Comparative proteomic analysis of Arthrobacter phenanthrenivorans Sphe3 on phenanthrene, phthalate and glucose

In the present study, by applying comparative quantitative proteomics, we investigated the metabolic adaptation of Arthrobacter phenanthrenivorans Sphe3 when using phenanthrene, phthalate, glucose or glucose plus phenanthrene as sole carbon and energy sources. More than a third of the total Sphe3 proteins, with function prediction within the genome, were identified with confidence. Proteomic analysis data and annotated genomic information coincide, allowing us to clarify the phenanthrene catabolic pathway. We confirmed the implication of several proteins in aromatic substrate degradation by identifying those mediating the initial ring-hydroxylation and ring cleavage of phenanthrene to phthalate, phthalate degradation, as well as ortho- and meta-protocatechuate catabolism. Repression of catabolic genes by glucose was observed by both proteomic and transcriptional analyses. The presence of aromatic substrates resulted in changes in the abundance of proteins involved in substrate and amino acid metabolism, stress response, detoxification and membrane and cell wall metabolism. Uptake and transport associated proteins differ in the substrates used, indicating the use of different uptake mechanisms for transport of each compound in the Sphe3 cells. Our results also suggest the activation of a glyoxylate shunt in the presence of aromatic compounds, based on the up-regulation of the key enzymes of this pathway.

BIOLOGICAL SIGNIFICANCE

A. phenanthrenivorans Sphe3, isolated from a creosote contaminated soil in Greece, can grow on phenanthrene as the sole source of carbon and energy. To explore the phenanthrene catabolic pathway by determining the key proteins involved in this pathway, as well as the global changes in proteins due to the adaptive response of Sphe3 cells grown on different substrates, we applied a gel-free quantitative proteomic analysis using nanoLC-MS/MS. To our knowledge this is the first study of comparative global proteomic changes occurring in the Sphe3 cells under exposure in different nutritional environments. The extended proteomic changes observed in Sphe3 grown on different substrates provide an insight in the complex interactions occurring in the presence of aromatic compounds and could serve as a basis for further investigations intended to elucidate the general regulatory mechanism by which Sphe3 adapts to such xenobiotic environments. This may light the way for more efficient engineering of bacteria towards more effective bioremediation applications.

Energy metabolism in Mycobacterium gilvum PYR-GCK: insights from transcript expression analyses following two states of induction

Mycobacterium gilvum PYR-GCK, a pyrene degrading bacterium, has been the subject of functional studies aimed at elucidating mechanisms related to its outstanding pollutant bioremediation/biodegradation activities. Several studies have investigated energy production and conservation in Mycobacterium, however, they all focused on the pathogenic strains using their various hosts as induction sources. To gain greater insight into Mycobacterium energy metabolism, mRNA expression studies focused on respiratory functions were performed under two different conditions using the toxic pollutant pyrene as a test substrate and glucose as a control substrate. This was done using two transcriptomic techniques: global transcriptomic RNA-sequencing and quantitative Real-Time PCR. Growth in the presence of pyrene resulted in upregulated expression of genes associated with limited oxygen or anaerobiosis in M. gilvum PYR-GCK. Upregulated genes included succinate dehydrogenases, nitrite reductase and various electron donors including formate dehydrogenases, fumarate reductases and NADH dehydrogenases. Oxidative phosphorylation genes (with respiratory chain complexes I, III -V) were expressed at low levels compared to the genes coding for the second molecular complex in the bacterial respiratory chain (fumarate reductase); which is highly functional during microaerophilic or anaerobic bacterial growth. This study reveals a molecular adaptation to a hypoxic mode of respiration during aerobic pyrene degradation. This is likely the result of a cellular oxygen shortage resulting from exhaustion of the oxygenase enzymes required for these degradation activities in M. gilvum PYR-GCK.

A gene expression study of the activities of aromatic ring-cleavage dioxygenases in Mycobacterium gilvum PYR-GCK to changes in salinity and pH during pyrene degradation

Polycyclic aromatic hydrocarbons (PAHs) are toxic pollutants found in the environment which can be removed through the use of physical and biological agents. The rate of PAH biodegradation is affected by environmental conditions of pH, salinity and temperature. Adaptation of the pyrene degrading bacteria, Mycobacterium gilvum PYR-GCK, to fluctuating environmental conditions during pyrene biodegrading activity was studied using the quantitative real time – Polymerase Chain Reaction (qRT-PCR) technique. Four aromatic ring-cleavage dioxygenase genes: phdF, phdI, pcaG and pcaH; critical to pyrene biodegradation, were studied in pH states of 5.5, 6.5, 7.5 and NaCl concentrations 0 M, 0.17 M, 0.5 M, 0.6 M, 1 M. First, we conducted a residual pyrene study using gas chromatography and flame ionization technologies. Central to a gene expression study is the use of a valid endogenous reference gene, making its determination our next approach, using the geNorm/NormFinder algorithms. Armed with a valid control gene, rpoB, we applied it to a gene expression study, using the comparative critical threshold (2^ΔΔCT) quantification method. The pyrene degrading activity of the strain was strongly functional in all the NaCl concentration states, with the least activity found at 1M (∼70% degraded after 48 hours of cultivation). The transcripts quantification of three genes backed this observation with high expression levels. The gene expression levels also revealed pH 6.5 as optimal for pyrene degradation and weak degradation activity at pH of 5.5, corroborating the residual pyrene analysis. The expression of these genes as proteins has already been studied in our laboratory using proteomics techniques and this validates our current study.